[ome-users] Zeiss czi format problems

[Melissa Linkert]

Hi Antonio,

> I encounter problems if I try to read the time stamp and positional
> information (stage information) of czi files generated from the ZEN
> software (ZEN2010 and ZEN2012).
> I can't retrieve the deltaT neither in the xml nor when using some
> of the Loci tools or reading the metadata.
> 
> I attach one example image and a little macro. May be you can tell
> me how to get this information out or what am I doing wrong.

Thank you for the bug report and example file.  Your macro is correct;
the problem is that the timestamps in the file are not detected.

We have a fix for this under review here:

https://github.com/openmicroscopy/bioformats/pull/562

The next release of Bio-Formats will solve the problem.

Regards,
-Melissa

On Mon, Jun 17, 2013 at 06:19:09PM +0200, politi wrote:
> Dear Bioformats and Loci users,
> I encounter problems if I try to read the time stamp and positional
> information (stage information) of czi files generated from the ZEN
> software (ZEN2010 and ZEN2012).
> I can't retrieve the deltaT neither in the xml nor when using some
> of the Loci tools or reading the metadata.
> 
> I attach one example image and a little macro. May be you can tell
> me how to get this information out or what am I doing wrong.
> 
> 
> Thanks
> 
> Antonio
> EMBL Heidelberg
> 
> 


> run("Close All")
> run("Bio-Formats Macro Extensions");
> Ext.openImagePlus("C:\\Users\\Antonio Politi\\Desktop\\Image2.czi");
> Ext.setId("C:\\Users\\Antonio Politi\\Desktop\\Image2.czi");
> //this function issues NAN
> Ext.getPlanePositionX(positionX, 0);
> print("PositionX " + positionX);
> //this does not read in
> Ext.getPlaneTimingDeltaT(deltaT, 0);
> print("DeltaT " + deltaT);
> 
> //this works
> Ext.getSizeX(sizeX);
> print("SizeX " + sizeX);
> Ext.getSizeT(sizeT);
> print("SizeT " + sizeT);
> 
> 

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